Research workbench
Inter-dimeric interface controls function and stability of S- methionine adenosyltransferase from U. urealiticum
Analyse Inter-dimeric interface controls function and stability of S- methionine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RK7
- Type
- protein
- Length
- 2,245 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine adenosyltransferase
- EC
- 2.5.1.6
- UniProt
- B2NE58
- Ligands
- SAM, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine adenosyltransferase (EC 2.5.1.6) | protein | 374 | 36% helix, 23% strand | B2NE58 |
| B, F | Methionine adenosyltransferase (EC 2.5.1.6) | protein | 374 | 35% helix, 23% strand | B2NE58 |
| E | Methionine adenosyltransferase (EC 2.5.1.6) | protein | 375 | 36% helix, 24% strand | B2NE58 |
| G | Methionine adenosyltransferase (EC 2.5.1.6) | protein | 375 | 35% helix, 23% strand | B2NE58 |
| H | Methionine adenosyltransferase (EC 2.5.1.6) | protein | 373 | 35% helix, 23% strand | B2NE58 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 12 copies · chains A, B, E, F, H, G
- CL · Chloride ion · ion · 6 copies · chains A, B, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.84 | 0.95 | 47 | SAM, CL |
| 2 | 277 | 0.84 | 0.95 | 49 | SAM, CL |
| 3 | 267 | 0.84 | 0.95 | 47 | SAM, CL |
| 4 | 278 | 0.83 | 0.95 | 47 | SAM, CL |
| 5 | 268 | 0.83 | 0.95 | 46 | SAM, CL |
Interfaces
9 interfaces between chains.
- E–F · 3276 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 3121 Ų buried · 49 hydrogen bonds · protein-protein
- G–H · 3044 Ų buried · 48 hydrogen bonds · protein-protein
- A–E · 780 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 660 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6RK7 · Inter-dimeric interface controls function and stability of S-methionine… · the same entry in another collection · chain F against F, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B2NE58
- Elsewhere: RCSB PDB 6RK7 · PDBe 6RK7 · UniProt B2NE58
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